Sequence
atgc intronic sequence ATGC exonic sequencegtattgtaagaacctattttatttttattctttttaattccaaattccttttttcctttcatatttttgtgtatttcttcatactgaaatgaccatatctgcatatgatatttatttttttctattcttatgtatgtcagaaataccaattacatcttttttttgtgacttaccagATAATTCGCCCAATGCGCTCCAAACATTGTCCAACTTGTAAGCACTGTGTTGAGCAGTTTGACCATCACTGTCCTTGGATATCAAATTGTGTTGGAAGG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g34860.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g34860.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA07G30380.1 (Glycine max), 3'ss of exon 9
gtattgtaagaacctattttatttttattctttttaattccaaattccttttttcctttcatatttttgtgtatttcttcatactgaaatgaccatatctgcatatgatatttatttttttctattcttatgtatgtcagaaataccaattacatcttttttttgtgacttaccagATAATTCGCCCAATGCGCTCCAAACATTGTCCAACTTGTAAGCACTGTGTTGAGCAGTTTGACCATCACTGTCCTTGGATATCAAATTGTGTTGGAAGG
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---------------------------------------------------gtttacatgatattcttttgagtatttaaaaaatctaatgttgatactttacttacatttctgtttattaaattctcaaaacaagtt---atcgcttatcaggttttctcgaattgtatcatcagATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTGGAACAGTTCGACCACCACTGTCCATGGATATCTAACTGTGTTGGGAAG
upper sequence: LOC_Os11g34860.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA08G06860.1 (Glycine max), 3'ss of exon 9
gtattgtaagaacctattttatttttattctttttaattccaaattccttttttcctttcatatttttgtgtatttcttcatactgaaatgaccata-tctgcatatgatatt-tatttttttctattcttatgtatgtcagaaataccaattacatcttttttttg---tgacttaccagATAATTCGCCCAATGCGCTCCAAACATTGTCCAACTTGTAAGCACTGTGTTGAGCAGTTTGACCATCACTGTCCTTGGATATCAAATTGTGTTGGAAGG
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---------------------------------------------------gttcacatgatattcttttgagtatttaaaaaatctaatgttgacactttacttacagttctgtattttactttattaaattctcaaaacaagttatcgcttatcaggttttctcgaattgtatcatcagATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTGGAACAGTTTGACCACCACTGTCCATGGATATCTAACTGTGTTGGGAAG
upper sequence: LOC_Os11g34860.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT2G14255.1 (Arabidopsis thaliana), 3'ss of exon 9
gtattgtaagaacctattttatttttattctttttaattccaaattccttttttcctttcatatttttgtgtatttcttcatactgaaatgaccatatctgcatatgatatttatttttttctattcttatgtatgtcagaaataccaattacatcttttttttgtgacttaccagATAATTCGCCCAATGCGCTCCAAACATTGTCCAACTTGTAAGCACTGTGTTGAGCAGTTTGACCATCACTGTCCTTGGATATCAAATTGTGTTGGAAGG
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----------------------------------------------------------------------gttttcctcaatcct--------tatttcaggggattacctcgatattttctttgttttct----------aactacaattatcattttttctt---------cagATAATTAGACCGGTGCGATCTAAGCACTGCCCCACTTGTAAGCGCTGCGTTGAACAGTTTGACCATCACTGCCCCTGGATTTCCAACTGTGTTGGTAAG
upper sequence: LOC_Os11g34860.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv03s0088g01260.t01 (Vitis vinifera), 3'ss of exon 9
gtattgtaagaacctattttatttttattctttttaattccaaattccttttttcctttcatatttttgtgtatttcttcatactgaaatgaccatatctgcatatgatatttatttttttctattcttatgtatgtcagaaataccaattacatcttttttttgtgacttaccagATAATTCGCCCAATGCGCTCCAAACATTGTCCAACTTGTAAGCACTGTGTTGAGCAGTTTGACCATCACTGTCCTTGGATATCAAATTGTGTTGGAAGG
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-----------------------------------------------------------gttttctcagtgaactttttctt--tcaaaagaacaga--tgcat-taatgcttgaaatactgt---cctaaacagatttggtgtgcattctcaatcttgttt------cttttcagATAATTAGACCTGTTCGCTCAAAGCACTGCCCTACATGTAAGCGCTGTGTGGAACAATTTGACCACCACTGCCCTTGGATTTCAAATTGTGTAGGGAAG
upper sequence: LOC_Os11g34860.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S70_186V6.2 (Physcomitrella patens), 3'ss of exon 11
gtattgtaagaacctattttatttttattctttttaattccaaattccttttttcctttcatatttttgtgtatttcttca--tactgaaatgaccatatctgca---tatgatatttatttttttctattcttatgtatgtca-gaaataccaa----ttacatcttttttttgtgacttaccagATAATTCGCCCAATGCGCTCCAAACATTGTCCAACTTGTAAGCACTGTGTTGAGCAGTTTGACCATCACTGTCCTTGGATATCAAATTGTGTTGGAAGG
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----------------gtttgtcagttcgattattcacctca--ttcgatttgatttcctaagttattagaaacctgttcgatcaatttaatggcttcttgaatagagtgctacatgtacttctttgtgtgctggagtaagtcttgatatccctagccgttgggtcatggttgcttg-ttcaatagATTGTGAGACCATTGCGATCCAAGCATTGCTCCTCATGCAACCGCTGTGTCGATCAATTTGACCATCATTGTCCTTGGATTTCAAATTGTGTTGGCAAG
upper sequence: LOC_Os11g34860.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ29308 (Selaginella moellendorffii), 3'ss of exon 3
gtattgtaagaacctattttatttttattctttttaattccaaattccttttttcctttcatatttttgtgtatttcttcatactgaaatgaccatatctgcatatgatatttatttttttctattcttatgtatgtcagaaataccaattacatcttttttttgtgacttaccagATAATTCGCCCAATGCGCTCCAAACATTGTCCAACTTGTAAGCACTGTGTTGAGCAGTTTGACCATCACTGTCCTTGGATATCAAATTGTGTTGGAAGG
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-------------------------------------------------------------------------------------------------------------gtagactaatttttgctttcatcttt--tagtcgttgtgagcaaatttttattg----------cagATAGTGAGGCCTGTAAGATCCAAGCACTGTTCGATTTGCAACCGCTGTGTAGAGCAGTTCGATCACCATTGTCCTTGGATATCAAACTGTGTTGGGAAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|27576416|gb|CA999110.1|CA999110EST: ATTCTTCTGCTTGGACAGGCAATTGGTCTCAGTTATGCCCCACATGCAAG ATAATTCGCCCAATGCGCTCCAAACATTGTCCAACTTGTAAGCACTGTGTT
genomic: ATTCTTCTGCTTGGACAGGCAATTGGTCTCAGTTATGCCCCACATGCAAGgtattgtaag ... gacttaccagATAATTCGCCCAATGCGCTCCAAACATTGTCCAACTTGTAAGCACTGTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctattcttatgtatgtcagaaataccaattacatcttttttttgtgacttaccagATAATTCGCCCAATGCGCTCCAAACATTGTCCAACTTGTAAGCACTGTGTTGAGCAGTTTGACCATCACTGTCCTTGGATATCAAATTGTGTTGGAAGG
aattacatcttttttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgtaagaacctattttatttttattctttttaattccaaattccttttttcctttcatatttttgtgtatttcttcatactgaaatgaccatatctgcatatgatatttatttttttctattcttatgtatgtcagaaataccaattacatcttttttttgtgacttaccagATAATTCGCCCAATGCGCTCCAAACATTGTCCAACTTGTAAGCACTGTGTTGAGCAGTTTGACCATCACTGTCCTTGGATATCAAATTGTGTTGGAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG